Population structure and genetic diversity of Polish Arabian horses based on pedigree data

With a history tracing back to at least the 18th century and a substantial global influence on various breeds, Polish Arabian horse population is of paramount importance for both breeders and conservationists. However, its genetic makeup and the population dynamics are still not well understood. This study presents an analysis of the modern Polish Arabian horse population using pedigree data, focusing on the breed's genetic diversity and population structure. Our analysis encompassed 1 498 individuals defined as the reference population (RP) and their 11 065 ancestors, which resulted in the dataset of 12 254 individuals (total population). We traced their genealogy to assess inbreeding coefficients (F), founder effects, and genetic variability measures such as the effective number of founders (fe), ancestors (fa), or founder genome equivalents (fge). The results indicated a good pedigree quality with an average of 28.1 maximum traced generations, revealing high pedigree completeness for initial generations with a decline beyond the seventh generation. The genetic diversity parameters showed a considerable bottleneck effect, with an effective number of founders at 73, which reflects a substantial loss of genetic diversity over time. Despite the vast total number of founders (852), only a few have had a lasting impact on the current population, signaling the need for revised breeding strategies to maintain diversity. The study identified a slight but consistent rise in inbreeding over the last century, with a marginal recent decline, and a significant difference in the contribution of various founders. The average F was 5.8%, with 99.6% of the reference population being inbred. The analysis of effective population size (Ne) highlighted potential risks for genetic diversity, urging for revision of breeding goals to consider a wider array of founder lineages. The study indicated that stallions belonging to RP can be attributed to 15 distinct sirelines, whereas mares to 45 unique damlines, more than considered in the current breeding program (8 and 15, respectively). Conclusively, the study underlines the need for ongoing monitoring and strategic breeding to maintain and enhance the genetic diversity of Polish Arabians, considering the breed's historical significance and contemporary genetic challenges.

Effect of obesity and hypothyroidism on hepcidin concentration in pregnancy - a pilot study using maternal and umbilical cord blood at delivery day

Hepcidin is a primary regulator of iron metabolism in the human body. By promoting ferroportin degradation, hepcidin reduces intestinal iron absorption and its release from intracellular stores. In the course of pregnancy, gradually declining hepcidin concentrations encourage placental iron transfer, thereby providing the appropriate amount of iron for fetal development. Hence, we aimed to investigate changes in maternal and cord blood hepcidin and iron metabolism parameters in normal-weight (n=17) and obese (n=17) gestating women, as well as gravid women with a history of hypothyroidism following the restoration of euthyroidism (n=17). All blood samples were taken on the day of delivery, and ELISA kits were used for measurements. A significant increase in maternal hepcidin concentration was observed in obese pregnant women, compared to normal-weight controls (29.53±4.20 ng/mL vs. 25.69±5.70 ng/mL; P<0.05). However, only a slight, insignificant tendency for lower hepcidin was noted in the hypothyroid group, compared to the healthy controls (23.10±6.00 ng/mL vs. 25.69±5.70 ng/mL; P=NS). Moreover, decreased maternal free triiodothyronine, triiodothyronine, free thyroxine, and ferritin levels were revealed in the hypothyroid group, compared to the normal-weight individuals (P<0.05). Furthermore, positive correlations between maternal hepcidin and the majority of maternal thyroid hormones were found, with a most potent relation to FT3 (r=0.40; P<0.01). Interestingly, no alterations of thyroid hormones and iron metabolism parameters were noticed in cord blood in any of the subgroups. In summary, pre-pregnancy obesity is associated with elevated maternal hepcidin, albeit no signs of lowered cord blood iron status were shown. Medical history of hypothyroidism following the restoration of euthyroidism does not substantially influence maternal nor cord blood hepcidin concentration, as well as fetal iron homeostasis, even though free thyroid hormone levels correlate with maternal hepcidin.

Differential fates of introns in gene expression due to global alternative splicing

The discovery of introns over four decades ago revealed a new vision of genes and their interrupted arrangement. Throughout the years, it has appeared that introns play essential roles in the regulation of gene expression. Unique processing of excised introns through the formation of lariats suggests a widespread role for these molecules in the structure and function of cells. In addition to rapid destruction, these lariats may linger on in the nucleus or may even be exported to the cytoplasm, where they remain stable circular RNAs (circRNAs). Alternative splicing (AS) is a source of diversity in mature transcripts harboring retained introns (RI-mRNAs). Such RNAs may contain one or more entire retained intron(s) (RIs), but they may also have intron fragments resulting from sequential excision of smaller subfragments via recursive splicing (RS), which is characteristic of long introns. There are many potential fates of RI-mRNAs, including their downregulation via nuclear and cytoplasmic surveillance systems and the generation of new protein isoforms with potentially different functions. Various reports have linked the presence of such unprocessed transcripts in mammals to important roles in normal development and in disease-related conditions. In certain human neurological-neuromuscular disorders, including myotonic dystrophy type 2 (DM2), frontotemporal dementia/amyotrophic lateral sclerosis (FTD/ALS) and Duchenne muscular dystrophy (DMD), peculiar processing of long introns has been identified and is associated with their pathogenic effects. In this review, we discuss different mechanisms involved in the processing of introns during AS and the functions of these large sections of the genome in our biology.

Obesity is associated with increased level of kisspeptin in mothers' blood and umbilical cord blood - a pilot study

OBJECTIVE

Kisspeptin (KP) is a major regulator of reproductive functions. It has also been shown to be involved in the metabolic changes associated with obesity. According to the well-established concept of prenatal programming, environmental factors can influence physiological and behavioral systems at the early stages of development. Thus, we hypothesized that in pregnant women, obesity can be associated with alterations in the levels of KP. We also assumed that the observed changes in obese mothers' blood (MB) would be reflected in the umbilical cord blood (CB).

MATERIALS AND METHODS

We collected MB and CB from obese and nonobese women and analyzed the differences in metabolic and hormonal profiles, including KP concentration, using commercially available assays.

RESULTS

We found that the level of KP was increased in the MB and CB of obese patients compared to nonobese subjects (p<0.05). A strong correlation was observed between the concentration of KP in MB and CB (r=0.8343; p<0.01). Moreover, we detected that the differences in the adipokine profile observed in the MB were not reflected in CB.

CONCLUSIONS

Our results indicate that blood KP concentration can serve as a valuable marker in pregnant women. However, further studies are needed to understand the alterations of this peptide in obese pregnant woman and their potential effects on offspring.

New PCR-specific markers for pollen fertility restoration QRfp-4R in rye (Secale cereale L.) with Pampa sterilizing cytoplasm

Pampa cytoplasmic male sterility phenomenon is used extensively in the rye hybrid breeding programs. It relies on sterilizing action of the cytoplasm resulting in non-viable pollen of female lines. The sterilizing effect is problematic for reversion, and efficient restores are needed. The most promising QTL is located on chromosome 4R, but other chromosomes may also code the trait. Advanced recombinant inbred lines formed bi-parental mapping population genotyped with DArTseq markers. Genetic mapping allowed the seven linkage groups to construct with numerous markers and represent all rye chromosomes. Single marker analysis and composite interval mapping were conducted to identify markers linked to the pollen fertility. Association mapping was used to detect additional markers associated with the trait. A highly significant QTL (QRfp-4R) that explained 42.3% of the phenotypic variation was mapped to the distal part of the long arm of the 4R chromosome. The markers localized in the QRfp-4R region achieve R² association values up to 0.59. The homology of the 43 marker sequences to the loci responsible for fertility restoration in other species and transcription termination factor (mTERF) linked to Rf genes was established. Ten markers were successfully converted into PCR-specific conditions, and their segregation pattern was identical to that of unconverted DArTs.

CDK12 inhibition reduces abnormalities in cells from patients with myotonic dystrophy and in a mouse model

Myotonic dystrophy type 1 (DM1) is an RNA-based disease with no current treatment. It is caused by a transcribed CTG repeat expansion within the 3' untranslated region of the dystrophia myotonica protein kinase (DMPK) gene. Mutant repeat expansion transcripts remain in the nuclei of patients' cells, forming distinct microscopically detectable foci that contribute substantially to the pathophysiology of the condition. Here, we report small-molecule inhibitors that remove nuclear foci and have beneficial effects in the HSA^LR mouse model, reducing transgene expression, leading to improvements in myotonia, splicing, and centralized nuclei. Using chemoproteomics in combination with cell-based assays, we identify cyclin-dependent kinase 12 (CDK12) as a druggable target for this condition. CDK12 is a protein elevated in DM1 cell lines and patient muscle biopsies, and our results showed that its inhibition led to reduced expression of repeat expansion RNA. Some of the inhibitors identified in this study are currently the subject of clinical trials for other indications and provide valuable starting points for a drug development program in DM1.

Role of hepcidin in physiology and pathophysiology. Emerging experimental and clinical evidence

Normal iron metabolism is an inherent feature of maintaining homeostasis. There is a wide range of iron disorders, which arise from iron deficiency or overload. In addition, disturbances in iron metabolism are observed in the course of numerous chronic diseases. Since iron is an essential constituent of hemoglobin, different types of anemia are clinical manifestations of both iron deficit or excess. This seemingly contradictory statement may be elucidated by the presence of hepcidin. Hepcidin is a primary regulator of iron metabolism in the human body. By promoting ferroportin degradation, hepcidin decreases the amount of iron in the circulation due to iron sequestration in the tissues and reduced intestinal absorption. Altered hepcidin concentration is a compensatory mechanism aimed at restoring iron homeostasis in various physiologic states, including pregnancy. However, hepcidin may also participate in the pathophysiologic background of hereditary hemochromatosis, anemia of chronic disease, myelodysplastic syndromes or β-thalassemia. Moreover, hepcidin is an acute-phase protein involved in innate immunity reactions. In our paper, we provide a comprehensive review of the physiologic and pathophysiologic functions of hepcidin. We present current knowledge on the structure, physiologic role and its expression control, as well as demonstrate the contribution of hepcidin in a state of illness. We also summarize the significance of hepcidin in normal and complicated pregnancy. Emphasizing the alterations in hepcidin upon treatment of specific diseases and their position in certain pathomechanisms, we support clinicians with practical aspects related to hepcidin.

Effects of a nine-strain bacterial synbiotic compared to simethicone in colicky babies - an open-label randomised study

The aim of the study was to determine effects of administration of simethicone and a multi-strain synbiotic on the crying behaviour of colicky babies. The study design consisted of an open-label, two parallel treatment group study involving 87 infants aged 3-6 weeks with infantile colic (defined as crying episodes lasting 3 or more hours per day and occurring at least 3 days per week within 3 weeks prior to enrolment) randomly, unequally [1:1.5] assigned to receive simethicone (n=33) or a multi-strain synbiotic (n=54) orally for 4 weeks. The multi-strain synbiotic contained Lactobacillus acidophilus LA-14, Lacticaseibacillus casei R0215, Lacticaseibacillus paracasei Lp-115, Lacticaseibacillus rhamnosus GG, Ligilactobacillus salivarius Ls-33, Bifidobacterium lactis Bl-04, Bifidobacterium bifidum R0071, Bifidobacterium longum R0175 and fructooligosaccharides). Primary outcome measures were the responder rates (effect ≥50% reduction from baseline) of the measures 'crying days last 3 weeks', 'average evening crying duration last 3 weeks' and 'reduction of average number of crying phases per day last three weeks' at the end of treatment. The study is registered at ClinicalTrials.gov under NCT04487834. Significantly higher responder rates (effect ≥50% reduction from baseline) of the multi-strain synbiotic compared to simethicone were found for the measures 'crying days last 3 weeks' (72% vs 18%, P<0.0001) and 'average evening crying duration last 3 weeks' (85% vs 39%, P=0.0001). No significant difference was found for the measure 'reduction of average number of crying phases per day last three weeks' (50% vs 42%, P=0.4852). No adverse effects were reported for the two treatment groups. Based on these results, the multi-strain synbiotic can be considered as an interesting therapeutic possibility for the treatment of infantile colic, worthwhile to be investigated further in non-clinical and clinical studies.

Reperfusion injury as a target for diminishing infarct size

Therapies for preventing reperfusion injury (RI) have been widely studied. However, the attempts to transfer cardioprotective therapies for reducing RI from experiments into clinical practice have been so far unsuccessful. Pathophysiological mechanisms of RI are complicated and compose of many pathways e.g. hypercontracture-mediated sarcolemma rupture, mitochondrial permeability transition pore persistent opening, reactive oxygen species formation, inflammation and no-reflow phenomenon. Based on research, it cannot be determined which mechanism dominates, probably they cooperate with a domination of one or another in different clinical circumstances. Our hypothesis is, that only intervention that at the same time interferes with different (all?) pathways of RI may turn out to be effective in decreasing the final area of infarction.

Global Increase in Circular RNA Levels in Myotonic Dystrophy

Splicing aberrations induced as a consequence of the sequestration of muscleblind-like splicing factors on the dystrophia myotonica protein kinase transcript, which contains expanded CUG repeats, present a major pathomechanism of myotonic dystrophy type 1 (DM1). As muscleblind-like factors may also be important factors involved in the biogenesis of circular RNAs (circRNAs), we hypothesized that the level of circRNAs would be decreased in DM1. To test this hypothesis, we selected 20 well-validated circRNAs and analyzed their levels in several experimental systems (e.g., cell lines, DM muscle tissues, and a mouse model of DM1) using droplet digital PCR assays. We also explored the global level of circRNAs using two RNA-Seq datasets of DM1 muscle samples. Contrary to our original hypothesis, our results consistently showed a global increase in circRNA levels in DM1, and we identified numerous circRNAs that were increased in DM1. We also identified many genes (including muscle-specific genes) giving rise to numerous (>10) circRNAs. Thus, this study is the first to show an increase in global circRNA levels in DM1. We also provided preliminary results showing the association of circRNA level with muscle weakness and alternative splicing changes that are biomarkers of DM1 severity.

Small Molecules Which Improve Pathogenesis of Myotonic Dystrophy Type 1

Myotonic dystrophy type 1 (DM1) is the most common muscular dystrophy in adults for which there is currently no treatment. The pathogenesis of this autosomal dominant disorder is associated with the expansion of CTG repeats in the 3'-UTR of the DMPK gene. DMPK transcripts with expanded CUG repeats (CUGexpDMPK) are retained in the nucleus forming multiple discrete foci, and their presence triggers a cascade of toxic events. Thus far, most research emphasis has been on interactions of CUGexpDMPK with the muscleblind-like (MBNL) family of splicing factors. These proteins are sequestered by the expanded CUG repeats of DMPK RNA leading to their functional depletion. As a consequence, abnormalities in many pathways of RNA metabolism, including alternative splicing, are detected in DM1. To date, in vitro and in vivo efforts to develop therapeutic strategies for DM1 have mostly been focused on targeting CUGexpDMPK via reducing their expression and/or preventing interactions with MBNL1. Antisense oligonucleotides targeted to the CUG repeats in the DMPK transcripts are of particular interest due to their potential capacity to discriminate between mutant and normal transcripts. However, a growing number of reports describe alternative strategies using small molecule chemicals acting independently of a direct interaction with CUGexpDMPK. In this review, we summarize current knowledge about these chemicals and we describe the beneficial effects they caused in different DM1 experimental models. We also present potential mechanisms of action of these compounds and pathways they affect which could be considered for future therapeutic interventions in DM1.

Quantitative Methods to Monitor RNA Biomarkers in Myotonic Dystrophy

Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are human neuromuscular disorders associated with mutations of simple repetitive sequences in affected genes. The abnormal expansion of CTG repeats in the 3'-UTR of the DMPK gene elicits DM1, whereas elongated CCTG repeats in intron 1 of ZNF9/CNBP triggers DM2. Pathogenesis of both disorders is manifested by nuclear retention of expanded repeat-containing RNAs and aberrant alternative splicing. The precise determination of absolute numbers of mutant RNA molecules is important for a better understanding of disease complexity and for accurate evaluation of the efficacy of therapeutic drugs. We present two quantitative methods, Multiplex Ligation-Dependent Probe Amplification and droplet digital PCR, for studying the mutant DMPK transcript (DMPK^expRNA) and the aberrant alternative splicing in DM1 and DM2 human tissues and cells. We demonstrate that in DM1, the DMPK^expRNA is detected in higher copy number than its normal counterpart. Moreover, the absolute number of the mutant transcript indicates its low abundance with only a few copies per cell in DM1 fibroblasts. Most importantly, in conjunction with fluorescence in-situ hybridization experiments, our results suggest that in DM1 fibroblasts, the vast majority of nuclear RNA foci consist of a few molecules of DMPK^expRNA.

Analysis of facial expressions in patients with schziophrenia, in comparison with a healthy control - case study

INTRODUCTION

Deficits in area of communication, crucial for maintaining proper social bonds, may have a prominent adverse impact on quality of life in patients with schizophrenia. Social exclusion, lack of employment and deterioration of family life, may be consequences of aggravated social competencies, caused by inability to properly exhibit and interpret facial expressions. Although this phenomenon is known since first clinical descriptions of schizophrenia, lack of proper methodology limited our knowledge in this area. Aim of our study was to compare facial expressivity of the patient with schizophrenia, and the healthy individual.

METHODS

47-years old patient suffering from schizophrenia, and 36-years old healthy individual were invited to participate in our study. They underwent the examination in Human Facial Modelling Lab in Polish-Japanese Institute of Information Technology in Bytom (Silesia, Katowice). Both participants were presented with two video materials, first one contained different facial expressions, which they had to imitate. Second one a part of comedy show, during which spontaneous reactions were recorded. Acquisition of facial expressions was conducted with marker-based technology of modelling. Obtained data was analyzed using Microsoft Excel.

RESULTS AND CONCLUSIONS

An overall facial expression intensity, expressed as an average value of distances traveled by markers during shifts from neutral position was higher in case of a healthy participant during both part of the study. The difference was especially visible in case of an upper half of the face. Utilization of marker-based methods in analysis of human facial expressions seem to be reliable and remarkably accurate.

The 30 kb deletion in the APOBEC3 cluster decreases APOBEC3A and APOBEC3B expression and creates a transcriptionally active hybrid gene but does not associate with breast cancer in the European population

APOBEC3B, in addition to other members of the APOBEC3 gene family, has recently been intensively studied due to its identification as a gene whose activation in cancer is responsible for a specific pattern of massively occurring somatic mutations. It was recently shown that a common large deletion in the APOBEC3 cluster (the APOBEC3B deletion) may increase the risk of breast cancer. However, conflicting evidence regarding this association was also reported. In the first step of our study, using different approaches, including an in-house designed multiplex ligation-dependent probe amplification assay, we analyzed the structure of the deletion and showed that although the breakpoints are located in highly homologous regions, which may generate recurrent occurrence of similar but not identical deletions, there is no sign of deletion heterogeneity. This knowledge allowed us to distinguish transcripts of all affected genes, including the highly homologous canonical APOBEC3A and APOBEC3B, and the hybrid APOBEC3A/APOBEC3B gene. We unambiguously confirmed the presence of the hybrid transcript and showed that the APOBEC3B deletion negatively correlates with APOBEC3A and APOBEC3B expression and positively correlates with APOBEC3A/APOBEC3B expression, whose mRNA level is >10-fold and >1500-fold lower than the level of APOBEC3A and APOBEC3B, respectively. In the next step, we performed a large-scale association study in three different cohorts (2972 cases and 3682 controls) and showed no association of the deletion with breast cancer, familial breast cancer or ovarian cancer. Further, we conducted a meta-analysis that confirmed the lack of the association of the deletion with breast cancer in non-Asian populations.

(CCUG)n RNA toxicity in a Drosophila model of myotonic dystrophy type 2 (DM2) activates apoptosis

The myotonic dystrophies are prototypic toxic RNA gain-of-function diseases. Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are caused by different unstable, noncoding microsatellite repeat expansions – (CTG)_DM1 in DMPK and (CCTG)_DM2 in CNBP. Although transcription of mutant repeats into (CUG)_DM1 or (CCUG)_DM2 appears to be necessary and sufficient to cause disease, their pathomechanisms remain incompletely understood. To study the mechanisms of (CCUG)_DM2 toxicity and develop a convenient model for drug screening, we generated a transgenic DM2 model in the fruit fly Drosophila melanogaster with (CCUG)_n repeats of variable length (n=16 and 106). Expression of noncoding (CCUG)₁₀₆, but not (CCUG)₁₆, in muscle and retinal cells led to the formation of ribonuclear foci and mis-splicing of genes implicated in DM pathology. Mis-splicing could be rescued by co-expression of human MBNL1, but not by CUGBP1 (CELF1) complementation. Flies with (CCUG)₁₀₆ displayed strong disruption of external eye morphology and of the underlying retina. Furthermore, expression of (CCUG)₁₀₆ in developing retinae caused a strong apoptotic response. Inhibition of apoptosis rescued the retinal disruption in (CCUG)₁₀₆ flies. Finally, we tested two chemical compounds that have shown therapeutic potential in DM1 models. Whereas treatment of (CCUG)₁₀₆ flies with pentamidine had no effect, treatment with a PKR inhibitor blocked both the formation of RNA foci and apoptosis in retinae of (CCUG)₁₀₆ flies. Our data indicate that expression of expanded (CCUG)_DM2 repeats is toxic, causing inappropriate cell death in affected fly eyes. Our Drosophila DM2 model might provide a convenient tool for in vivo drug screening.

Summary: A Drosophila model of myotonic dystrophy type 2 (DM2) recapitulates several features of the human disease, identifies apoptosis as a contributing factor to DM2, and is likely to provide a convenient tool for drug screening.

Implementation of the MOTEK CAREN system in behavioural therapy for patients with anxiety disorders

BACKGROUND

Virtual reality exposure therapy (VRET) is becoming a more and more popular treatment method for patients suffering from anxiety disorders. One of the VRET methods, wchich could be used for this group of patients is MOTEK CAREN system, however, so far no studies have been published on its implementation in psychiatric disorders.

SUBJECT AND METHODS

Presented here is a case of a 45 year old woman suffering from anxiety disorders, who underwent a series of four subsequent trainings with the use of MOTEK CAREN system repeted once a week. Data from the system were collected on the work of muscles, joints, reactions of the ground, etc. Blood pressure, pulse and salivary cortisol level were measured before and after each training. The level of state and trait anxiety was each time measured with the STAI inventory.

RESULTS

The changes of the values of heart rate, blood pressure and salivary cortisol suggest that all trainings we stressful events for the patients, as they were not observed in the control session. But the gradual decrease in the levels of salivary cortisol and axiety as state after subsequent trainings may be signs of a gradual adaptation of the patient to the stressful situation. A lower cadence during the trainings compared to the control session was observed, however the speed of the cadence increased with each session.

CONCLUSIONS

Ttrainings with the MOTEK CAREN system can be promising in the treatment of anxiety disorders. Of course in order to draw more evidence based conclusions this observations must be confirmed on a larger sample of patients.

Oncogenomic portals for the visualization and analysis of genome-wide cancer data

Somatically acquired genomic alterations that drive oncogenic cellular processes are of great scientific and clinical interest. Since the initiation of large-scale cancer genomic projects (e.g., the Cancer Genome Project, The Cancer Genome Atlas, and the International Cancer Genome Consortium cancer genome projects), a number of web-based portals have been created to facilitate access to multidimensional oncogenomic data and assist with the interpretation of the data. The portals provide the visualization of small-size mutations, copy number variations, methylation, and gene/protein expression data that can be correlated with the available clinical, epidemiological, and molecular features. Additionally, the portals enable to analyze the gathered data with the use of various user-friendly statistical tools. Herein, we present a highly illustrated review of seven portals, i.e., Tumorscape, UCSC Cancer Genomics Browser, ICGC Data Portal, COSMIC, cBioPortal, IntOGen, and BioProfiling.de. All of the selected portals are user-friendly and can be exploited by scientists from different cancer-associated fields, including those without bioinformatics background. It is expected that the use of the portals will contribute to a better understanding of cancer molecular etiology and will ultimately accelerate the translation of genomic knowledge into clinical practice.

Decreased effectiveness of ischemic heart preconditioning in the state of chronic inflammation

There is growing evidence, that beneficial effects of ischemic heart preconditioning (IPC) may be lost or limited due to diabetes, hyperlipidemia, hypertension, atherosclerosis, heart failure and senility. It is plausible, that these conditions interfere with the biochemical pathways underlying the IPC response, but the detailed explanation is not clear. Pro-inflammatory cytokines (IL-1β, IL-6, TNF-α), monocyte chemotactic protein-1 (MCP-1), histamine and many other agents used in a single dose before prolonged ischemia mimic IPC. However prolonged exposure to preconditioning mimetics leads to tolerance (tachyphylaxis). In the state of such tolerance ischemic preconditioning is no longer protective. Studies suggest that diabetes, hyperlipidemia, hypertension, atherosclerosis, heart failure and older age are accompanied by increased plasma levels of pro-inflammatory cytokines, MCP-1 and other inflammatory mediators. Therefore, we raised the hypothesis, that the reported lack of benefits of IPC in the listed states may be due to tolerance to IPC developed during prolonged exposure of the myocardium to preconditioning mimetics.

Cooperation meets competition in microRNA-mediated DMPK transcript regulation

The fundamental role of microRNAs (miRNAs) in the regulation of gene expression has been well-established, but many miRNA-driven regulatory mechanisms remain elusive. In the present study, we demonstrate that miRNAs regulate the expression of DMPK, the gene mutated in myotonic dystrophy type 1 (DM1), and we provide insight regarding the concerted effect of the miRNAs on the DMPK target. Specifically, we examined the binding of several miRNAs to the DMPK 3′ UTR using luciferase assays. We validated the interactions between the DMPK transcript and the conserved miR-206 and miR-148a. We suggest a possible cooperativity between these two miRNAs and discuss gene targeting by miRNA pairs that vary in distance between their binding sites and expression profiles. In the same luciferase reporter system, we showed miR-15b/16 binding to the non-conserved CUG repeat tract present in the DMPK transcript and that the CUG-repeat-binding miRNAs might also act cooperatively. Moreover, we detected miR-16 in cytoplasmic foci formed by exogenously expressed RNAs with expanded CUG repeats. Therefore, we propose that the expanded CUGs may serve as a target for concerted regulation by miRNAs and may also act as molecular sponges for natural miRNAs with CAG repeats in their seed regions, thereby affecting their physiological functions.

RAN translation and frameshifting as translational challenges at simple repeats of human neurodegenerative disorders

Repeat-associated disorders caused by expansions of short sequences have been classified as coding and noncoding and are thought to be caused by protein gain-of-function and RNA gain-of-function mechanisms, respectively. The boundary between such classifications has recently been blurred by the discovery of repeat-associated non-AUG (RAN) translation reported in spinocerebellar ataxia type 8, myotonic dystrophy type 1, fragile X tremor/ataxia syndrome and C9ORF72 amyotrophic lateral sclerosis and frontotemporal dementia. This noncanonical translation requires no AUG start codon and can initiate in multiple frames of CAG, CGG and GGGGCC repeats of the sense and antisense strands of disease-relevant transcripts. RNA structures formed by the repeats have been suggested as possible triggers; however, the precise mechanism of the translation initiation remains elusive. Templates containing expansions of microsatellites have also been shown to challenge translation elongation, as frameshifting has been recognized across CAG repeats in spinocerebellar ataxia type 3 and Huntington's disease. Determining the critical requirements for RAN translation and frameshifting is essential to decipher the mechanisms that govern these processes. The contribution of unusual translation products to pathogenesis needs to be better understood. In this review, we present current knowledge regarding RAN translation and frameshifting and discuss the proposed mechanisms of translational challenges imposed by simple repeat expansions.

Small molecule kinase inhibitors alleviate different molecular features of myotonic dystrophy type 1

Expandable (CTG)n repeats in the 3′ UTR of the DMPK gene are a cause of myotonic dystrophy type 1 (DM1), which leads to a toxic RNA gain-of-function disease. Mutant RNAs with expanded CUG repeats are retained in the nucleus and aggregate in discrete inclusions. These foci sequester splicing factors of the MBNL family and trigger upregulation of the CUGBP family of proteins resulting in the mis-splicing of their target transcripts. To date, many efforts to develop novel therapeutic strategies have been focused on disrupting the toxic nuclear foci and correcting aberrant alternative splicing via targeting mutant CUG repeats RNA; however, no effective treatment for DM1 is currently available. Herein, we present results of culturing of human DM1 myoblasts and fibroblasts with two small-molecule ATP-binding site-specific kinase inhibitors, C16 and C51, which resulted in the alleviation of the dominant-negative effects of CUG repeat expansion. Reversal of the DM1 molecular phenotype includes a reduction of the size and number of foci containing expanded CUG repeat transcripts, decreased steady-state levels of CUGBP1 protein, and consequent improvement of the aberrant alternative splicing of several pre-mRNAs misregulated in DM1.

Triplet repeat RNA structure and its role as pathogenic agent and therapeutic target

This review presents detailed information about the structure of triplet repeat RNA and addresses the simple sequence repeats of normal and expanded lengths in the context of the physiological and pathogenic roles played in human cells. First, we discuss the occurrence and frequency of various trinucleotide repeats in transcripts and classify them according to the propensity to form RNA structures of different architectures and stabilities. We show that repeats capable of forming hairpin structures are overrepresented in exons, which implies that they may have important functions. We further describe long triplet repeat RNA as a pathogenic agent by presenting human neurological diseases caused by triplet repeat expansions in which mutant RNA gains a toxic function. Prominent examples of these diseases include myotonic dystrophy type 1 and fragile X-associated tremor ataxia syndrome, which are triggered by mutant CUG and CGG repeats, respectively. In addition, we discuss RNA-mediated pathogenesis in polyglutamine disorders such as Huntington's disease and spinocerebellar ataxia type 3, in which expanded CAG repeats may act as an auxiliary toxic agent. Finally, triplet repeat RNA is presented as a therapeutic target. We describe various concepts and approaches aimed at the selective inhibition of mutant transcript activity in experimental therapies developed for repeat-associated diseases.

CAG repeats mimic CUG repeats in the misregulation of alternative splicing

Mutant transcripts containing expanded CUG repeats in the untranslated region are a pathogenic factor in myotonic dystrophy type 1 (DM1). The mutant RNA sequesters the muscleblind-like 1 (MBNL1) splicing factor and causes misregulation of the alternative splicing of multiple genes that are linked to clinical symptoms of the disease. In this study, we show that either long untranslated CAG repeat RNA or short synthetic CAG repeats induce splicing aberrations typical of DM1. Alternative splicing defects are also caused by translated CAG repeats in normal cells transfected with a mutant ATXN3 gene construct and in cells derived from spinocerebellar ataxia type 3 and Huntington's disease patients. Splicing misregulation is unlikely to be caused by traces of antisense transcripts with CUG repeats, and the possible trigger of this misregulation may be sequestration of the MBNL1 protein with nuclear RNA inclusions containing expanded CAG repeat transcripts. We propose that alternative splicing misregulation by mutant CAG repeats may contribute to the pathological features of polyglutamine disorders.

Cellular toxicity of expanded RNA repeats: focus on RNA foci

Discrete and punctate nuclear RNA foci are characteristic molecular hallmarks of pathogenesis in myotonic dystrophy type 1 and type 2. Intranuclear RNA inclusions of distinct morphology have also been found in fragile X-associated tremor ataxia syndrome, Huntington's disease-like 2, spinocerebellar ataxias type 8, type 10 and type 31. These neurological diseases are associated with the presence of abnormally long simple repeat expansions in their respective genes whose expression leads to the formation of flawed transcripts with altered metabolisms. Expanded CUG, CCUG, CGG, CAG, AUUCU and UGGAA repeats are associated with the diseases and accumulate in nuclear foci, as demonstrated in variety of cells and tissues of human and model organisms. These repeat RNA foci differ in size, shape, cellular abundance and protein composition and their formation has a negative impact on cellular functions. This review summarizes the efforts of many laboratories over the past 15 years to characterize nuclear RNA foci that are recognized as important triggers in the mutant repeat RNA toxic gain-of-function mechanisms of pathogenesis in neurological disorders.

CAG repeat RNA as an auxiliary toxic agent in polyglutamine disorders

Over 20 genetic loci with abnormal expansions of short tandem repeats have been associated with human hereditary neurological diseases. Of these, specific trinucleotide repeats located in non-coding and coding regions of individual genes implicated in these disorders are strongly overrepresented. Expansions of CTG, CGG and CAG repeats are linked to, respectively, myotonic dystrophy type 1 (DM1), fragile X-associated tremor/ataxia syndrome (FXTAS), as well as Huntington's disease (HD) and a number of spinocerebellar ataxias (SCAs). Expanded CAG repeats in translated exons trigger the most disorders for which a protein gain-of-function mechanism has been proposed to explain neurodegeneration by polyglutamine-rich (poly-Q) proteins. However, the results of last years showed that RNA composed of mutated CAG repeats can also be toxic and contribute to pathogenesis of polyglutamine disorders through an RNA-mediated gain-of-function mechanism. This mechanism has been best characterized in the non-coding repeat disorder DM1 and is also implicated in several other diseases, such as FXTAS, spinocerebellar ataxia type 8 (SCA8), Huntington's disease-like 2 (HDL2), as well as in myotonic dystrophy type 2 (DM2), spinocerebellar ataxia type 10 (SCA10) and type 31 (SCA31). In this review, we summarize recent findings that emphasize the participation of coding mutant CAG repeat RNA in the pathogenesis of polyglutamine disorders, and we discuss the basis of an RNA gain-of-function model in non-coding diseases such as DM1, FXTAS and SCA8.

Mutant CAG repeats of Huntingtin transcript fold into hairpins, form nuclear foci and are targets for RNA interference

The CAG repeat expansions that occur in translated regions of specific genes can cause human genetic disorders known as polyglutamine (poly-Q)-triggered diseases. Huntington's disease and spinobulbar muscular atrophy (SBMA) are examples of these diseases in which underlying mutations are localized near other trinucleotide repeats in the huntingtin (HTT) and androgen receptor (AR) genes, respectively. Mutant proteins that contain expanded polyglutamine tracts are well-known triggers of pathogenesis in poly-Q diseases, but a toxic role for mutant transcripts has also been proposed. To gain insight into the structural features of complex triplet repeats of HTT and AR transcripts, we determined their structures in vitro and showed the contribution of neighboring repeats to CAG repeat hairpin formation. We also demonstrated that the expanded transcript is retained in the nucleus of human HD fibroblasts and is colocalized with the MBNL1 protein. This suggests that the CAG repeats in the HTT mRNA adopt ds-like RNA conformations in vivo. The intracellular structure of the CAG repeat region of mutant HTT transcripts was not sufficiently stable to be protected from cleavage by an siRNA targeting the repeats and the silencing efficiency was higher for the mutant transcript than for its normal counterpart.

[Modifications of the cytoimmunological pattern of bronchoalveolar lavage (BAL) material caused by cigarette smoking in selected lower air-way diseases]

INTRODUCTION

In the last years we have used flow cytometry as an auxiliary diagnostic tool in alveolar lymphocyte (i.e. originating from BAL) phenotyping in more than 500 persons suspected for lower airways pathology.

MATERIAL AND METHODS

In the study we compared the results of 1) BAL lymphocyte typing by flow cytometry, 2) cytological examination, respectively, in nonsmoking/smoking (NS/S) patients with lung sarcoidosis, n = 56/31, extrinsic allergic alveolitis (EAA), n = 9/5, silicosis, n = 15/18, idiopathic pulmonary fibrosis (IPF), n = 20/7, and pulmonary tuberculosis (TBC), n = 7/6. The results were related to the volume of BAL fluid recovery (higher value reflects the dominance of lower airways content versus bronchial content).

RESULTS

In smoking patients, in comparison with respective NS, significantly higher total BAL cell numer (except TBC), higher macrophage percentage, lower lymphocyte percentage and lower CD4/CD8 ratio (except EAA) was found. CD4/CD8 results: 8.26 +/- 0.52 (NS) vs 4.29 +/- 0.65 (S) in sarcoidosis (p < 0.001), 1.18 +/- 0.44 (NS) vs 0.99 +/- 0.43 (S) in IPF (p < 0.05), 1.79 +/- 0.22 (NS) vs 0.73 +/- 0.11 (S) in silicosis (p < 0.001) and 1.64 +/- 0.57 vs 0.88 +/- 0.1 in TBC (p < 0.05). Additionally, cigarette smoking modified BAL pattern: 1. in sarcoidosis and silicosis lower CD4+ cell and higher CD8+ cell percentage; 2. in IPF increase in neutrophil percentage; 3. in TBC higher neutrophil and eosinophil percentage. Both in NS and S, BAL fluid recovery rate is significantly positively correlated with CD4/CD8 ratio and total BAL CD3+ cell number and negatively with BAL CD8+ cell percentage.

CONCLUSIONS

Interpreting of BAL material cytoimmunology pattern should take into account data on cigarette smoking and BAL fluid recovery rate. The results obtained in the study may reflect more severe disease course in IPF and TBC.

Three different premixed combinations of biphasic insulin aspart - comparison of the efficacy and safety in a randomized controlled clinical trial in subjects with type 2 diabetes

AIM

To evaluate clinical efficacy and safety of biphasic insulin aspart (BIAsp) 30 twice daily (b.i.d.) vs. BIAsp 50 or BIAsp 70 (high-mix regimens) thrice daily (t.i.d.) all in combination with metformin in a 36-week clinical trial in subjects with type 2 diabetes.

METHODS

Efficacy measurements included haemoglobin A(1c) (HbA(1c)) and eight-point plasma glucose (PG); safety included adverse events (AEs) and hypoglycaemic episodes. The three treatment groups (approximately 200 subjects in each group) were well matched regarding sex ratio, ethnicity, age and body mass index.

RESULTS

After 12 weeks, 43% and 54% in the BIAsp 50 and 70 groups, respectively, switched their dinner insulin to BIAsp 30. Both high-mix regimens were non-inferior to BIAsp 30 b.i.d., as measured by change in HbA(1c), and the BIAsp %50 regimen was superior. The odds for meeting the American Diabetes Association and The American Association of Clinícal Endocrinologist HbA(1c) targets of <7% and < or =6.5%, respectively, were significantly higher with the BIAsp 50 regimen than with BIAsp 30. A significantly lower PG level was achieved from lunch until 02:00 hours with both high-mix regimens compared with BIAsp 30 b.i.d. AEs were mild or moderate with all three regimens. Frequency of hypoglycaemic episodes was comparable for the BIAsp 50 and the BIAsp 30 b.i.d. regimens but was significantly higher with BIAsp 70 t.i.d.

CONCLUSIONS

Glycaemic control improved with BIAsp 50 t.i.d. without higher incidence of hypoglycaemia compared with BIAsp 30 b.i.d.; with BIAsp 70 t.i.d. lower PG levels from lunch to 02.00 hours, but more hypoglycaemic episodes were obtained compared with BIAsp 30 b.i.d.

Non-B DNA conformations formed by long repeating tracts of myotonic dystrophy type 1, myotonic dystrophy type 2, and Friedreich's ataxia genes, not the sequences per se, promote mutagenesis in flanking regions

The expansions of long repeating tracts of CTG.CAG, CCTG.CAGG, and GAA.TTC are integral to the etiology of myotonic dystrophy type 1 (DM1), myotonic dystrophy type 2 (DM2), and Friedreich's ataxia (FRDA). Essentially all studies on the molecular mechanisms of this expansion process invoke an important role for non-B DNA conformations which may be adopted by these repeat sequences. We have directly evaluated the role(s) of the repeating sequences per se, or of the non-B DNA conformations formed by these sequences, in the mutagenic process. Studies in Escherichia coli and three types of mammalian (COS-7, CV-1, and HEK-293) fibroblast-like cells revealed that conditions which promoted the formation of the non-B DNA structures enhanced the genetic instabilities, both within the repeat sequences and in the flanking sequences of up to approximately 4 kbp. The three strategies utilized included: the in vivo modulation of global negative supercoil density using topA and gyrB mutant E. coli strains; the in vivo cleavage of hairpin loops, which are an obligate consequence of slipped-strand structures, cruciforms, and intramolecular triplexes, by inactivation of the SbcC protein; and by genetic instability studies with plasmids containing long repeating sequence inserts that do, and do not, adopt non-B DNA structures in vitro. Hence, non-B DNA conformations are critical for these mutagenesis mechanisms.

The involvement of non-B DNA structures in gross chromosomal rearrangements

Non-B DNA conformations adopted by certain types of DNA sequences promote genetic instabilities, especially gross rearrangements including translocations. We conclude the following: (a) slipped (hairpin) structures, cruciforms, triplexes, tetraplexes and i-motifs, and left-handed Z-DNA are formed in chromosomes and elicit profound genetic consequences via recombination-repair, (b) repeating sequences, probably in their non-B conformations, cause gross genomic rearrangements (translocations, deletions, insertions, inversions, and duplications), and (c) these rearrangements are the genetic basis for numerous human diseases including polycystic kidney disease, adrenoleukodystrophy, follicular lymphomas, and spermatogenic failure.

Implications of the Facing Dementia Survey for the general population, patients and caregivers across Europe

The Facing Dementia Survey included interviews with approximately 1200 members of the general public, 600 persons who served as primary caregivers for a person with Alzheimer's disease (AD) and 96 persons with AD. Members of the general public and the caregivers indicated level of agreement on a 5-point scale to a series of attitudinal statements about the disease as well as other diagnostic questions. Persons with AD underwent a qualitative interview. Results indicate that Europeans are acutely aware of the potentially devastating consequences of AD, but few are familiar with the early-stage symptoms. Most members of the general population accept that early intervention and therapy are key to slowing the effects of the disease. Caregivers often delayed consulting a physician about a loved one's behaviour, partly because of uncertainty about early signs of AD. They also expressed doubt about the ability of physicians to make the diagnosis. Caregivers experience profound effects of AD in every area of their life--emotional, physical, social and financial. Persons with AD responded to their diagnosis in one of three ways: a fatalistic attitude, a belief that their problems are linked to old age or a lack of acceptance. Survey respondents from three populations were critical of the level of government investment in and support of AD.

The Myotonic Dystrophy Type 1 Triplet Repeat Sequence Induces Gross Deletions and Inversions

The capacity of (CTG.CAG)n and (GAA.TTC)n repeat tracts in plasmids to induce mutations in DNA flanking regions was evaluated in Escherichia coli. Long repeats of these sequences are involved in the etiology of myotonic dystrophy type 1 and Friedreich's ataxia, respectively. Long (CTG.CAG)n (where n = 98 and 175) caused the deletion of most, or all, of the repeats and the flanking GFP gene. Deletions of 0.6-1.8 kbp were found as well as inversions. Shorter repeat tracts (where n = 0 or 17) were essentially inert, as observed for the (GAA.TTC)176-containing plasmid. The orientation of the triplet repeat sequence (TRS) relative to the unidirectional origin of replication had a pronounced effect, signaling the participation of replication and/or repair systems. Also, when the TRS was transcribed, the level of deletions was greatly elevated. Under certain conditions, 30-50% of the products contained gross deletions. DNA sequence analyses of the breakpoint junctions in 47 deletions revealed the presence of 1-8-bp direct or inverted homologies in all cases. Also, the presence of non-B folded conformations (i.e. slipped structures, cruciforms, or triplexes) at or near the breakpoints was predicted in all cases. This genetic behavior, which was previously unrecognized for a TRS, may provide the basis for a new type of instability of the myotonic dystrophy protein kinase (DMPK) gene in patients with a full mutation.

Endosperm degradation during seed development of Echinocystis lobata (Cucurbitaceae) as a manifestation of programmed cell death (PCD) in plants

Programmed cell death (PCD) is an active, genetically controlled process that ultimately leads to elimination of unnecessary or damaged cells from multicellular organism. It occurs during normal growth and development or in response to a variety of environmental triggers and is indispensable for survival of the organism. In Echinocystis lobata the endosperm, an ephemeral tissue in angiosperm plants, undergoes distinct cytological, physiological and molecular changes during seed development and maturation. As a result, mature seeds are deprived of this tissue. The endosperm was analyzed at the consecutive stages of seed development. The morphological changes of cells were studied at light and electron microscope levels. In this paper we report that endosperm cells undergo morphological and biochemical changes characteristic of apoptosis, a particular type of PCD, i.e. cell shrinkage, chromatin condensation, nuclear fragmentation, and cytoplasm degradation, while the ultrastructure of mitochondria seems to be less changed. Furthermore, the progression of DNA degradation has been shown by agarose gel electrophoresis (ladder pattern of DNA fragmentseparation), TUNEL and comet assay. It isconcluded that during seed maturation, endosperm degradation process is accompanied by typical PCD-related changes of cell morphology and internucleosomal DNA cleavage.

[Comparison of types and drug sensitivity of bacteria isolated from sputum and bronchoscopic material. Analysis of results from routine diagnostic tests from 1995-1997]

Proper identification of the organism and determination of their sensitivity to antimicrobial agents, is the most important part of the management of patients with symptoms of respiratory system infections. In the case of pulmonary infections, the utility of sputum for diagnosing the cause of lower respiratory tract infections seems to be limited. In the patients receiving antibiotics, there is a high rate of colonization of the upper respiratory tract that may lead to the overgrowth of one or an other pathogen, making it more abundant in the upper than an lower respiratory tract. Also, the patients may be unable to provide adequate lower-respiratory-tract samples. For these reason, more invasive procedures have been recommended. These include bronchoscopy with bronchoalveolar lavage (BAL) sampling. The purpose of our study was to determine the value of sputum and BAL fluid on the basis of profile bacteria and their drug sensitivity isolated from the patients treated in Nat. Res. Inst. Tuber. and Lung Diseases in Warsaw during period of 3 years (1995-1997). On the basis of analysis of 5926 sputum samples and 3534 bronchoscopic materials we have found that the bacterial pathogens species and drug resistant pattern were similar in sputum samples as in materials of bronchoscopic procedures. The same bacterial species and numbers Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus were predominant in both type of clinical materials with near the same frequency.

Allogeneic and autologous bone marrow transplantation in single centre experience

Among 290 BMT procedures: 74 AML, 78 ALL, 34 CML, 6 SAA, 3 MDS, 42 HD, 35 NHL, 11 MM, and 7 solid tumours (breast or testis cancer) Allogeneic BMT was performed in 76 patients and ABMT/APBCT in 214 patients. Survival, DFS and relapse curves were calculated using the Kaplan-Meier product limit method. Variables potentially affecting survival and DFS were assessed in a multivariate analysis by the Cox proportional hazard model in a stepwise regression. The promising results were obtained in high risk adult ALL in the first CR. DFS in CR1 patients transplanted after full dose induction and high dose consolidation was significantly longer if compared to those who received dose/time reduced or postponed treatment. For CR> or =2 patients and with CNS involvement at diagnosis ABMT offers a salvage therapy that needs further improvement. In relapsed and refractory HD better results are obtained in patients relapsing > 1 year after first CR and in patients with entirely nodal localisation of this relapse. In NHL bone marrow and spleen infiltration at diagnosis appear to be an unfavourable prognostic factor.